In this study, we investigate the intricate interplay of working hours and perceived health, and its subsequent influence on gender wage disparity in South Korea. Drawing from the Korean Labor and Income Panel Study (KLIPS) spanning 2013 to 2021, a causal link between working hours and perceived health is established. Employing cross-lagged and instrumental variable approaches, this study highlights the distinct health impacts of working hours on men and women, resulting in gender-specific wage differences. The 2018 policy amendment in South Korea, which lowered the maximum weekly working hours, served as an instrumental variable. Key findings reveal an inverted U-curve relationship between working hours and health, with discerned inflection points at 41.36 hours per week for men and 28.95 hours for women. Additionally, our analysis uncovers a bidirectional relationship between self-perceived health and earnings. Consequently, prolonged work durations have a more pronounced negative impact on women's health, which might contribute to wage discrepancies. In summary, South Korea's 2018 initiative to curtail weekly working hours might play a pivotal role in narrowing both the health and wage disparities between genders. As the workforce transitions towards schedules that prioritize individual health boundaries, it is plausible to anticipate a progression towards more balanced health and wage outcomes across genders in the South Korean work environment.